Rapid and accurate assembly of new ribosomal subunits is essential for cell growth. Here we show that the ribosomal proteins make assembly more cooperative by discriminating against non-native conformations of the Escherichia coli 16S ribosomal RNA. We used hydroxyl radical footprinting to measure how much the proteins stabilize individual ribosomal RNA tertiary interactions, revealing the free-energy landscape for assembly of the 16S 5' domain. When ribosomal proteins S4, S17 and S20 bind the 5' domain RNA, a native and a non-native assembly intermediate are equally populated. The secondary assembly protein S16 suppresses the non-native intermediate, smoothing the path to the native complex. In the final step of 5' domain assembly, S16 drives a conformational switch at helix 3 that stabilizes pseudoknots in the 30S decoding center. Long-range communication between the S16 binding site and the decoding center helps to explain the crucial role of S16 in 30S assembly.